Starting phenix.real_space_refine on Mon Jan 13 20:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqo_60386/01_2025/8zqo_60386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqo_60386/01_2025/8zqo_60386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqo_60386/01_2025/8zqo_60386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqo_60386/01_2025/8zqo_60386.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqo_60386/01_2025/8zqo_60386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqo_60386/01_2025/8zqo_60386.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2683 2.51 5 N 607 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4032 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3959 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CL': 1, ' NA': 2, 'HC6': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 3.26, per 1000 atoms: 0.81 Number of scatterers: 4032 At special positions: 0 Unit cell: (85, 75.65, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 20 16.00 Na 2 11.00 O 719 8.00 N 607 7.00 C 2683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 480.4 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.742A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.521A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.704A pdb=" N GLY A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.553A pdb=" N ALA A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.540A pdb=" N TRP A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.520A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 4.622A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 130 through 157 removed outlier: 4.301A pdb=" N ALA A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.602A pdb=" N TYR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.844A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix removed outlier: 3.601A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 262 removed outlier: 4.342A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 285 Processing helix chain 'A' and resid 285 through 297 removed outlier: 3.610A pdb=" N ILE A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.543A pdb=" N THR A 303 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.674A pdb=" N CYS A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 3.693A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 401 through 427 removed outlier: 4.159A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.546A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 478 through 504 removed outlier: 3.503A pdb=" N LEU A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 282 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 601 1.31 - 1.43: 1178 1.43 - 1.56: 2328 1.56 - 1.68: 1 1.68 - 1.81: 35 Bond restraints: 4143 Sorted by residual: bond pdb=" C LEU A 97 " pdb=" O LEU A 97 " ideal model delta sigma weight residual 1.237 1.180 0.056 1.19e-02 7.06e+03 2.23e+01 bond pdb=" CA LEU A 97 " pdb=" C LEU A 97 " ideal model delta sigma weight residual 1.524 1.466 0.057 1.29e-02 6.01e+03 1.97e+01 bond pdb=" CAJ HC6 A 603 " pdb=" CAM HC6 A 603 " ideal model delta sigma weight residual 1.475 1.404 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N VAL A 402 " pdb=" CA VAL A 402 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.47e+00 bond pdb=" N GLN A 370 " pdb=" CA GLN A 370 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 6.86e+00 ... (remaining 4138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 5505 1.80 - 3.59: 112 3.59 - 5.39: 28 5.39 - 7.18: 11 7.18 - 8.98: 9 Bond angle restraints: 5665 Sorted by residual: angle pdb=" O ALA A 26 " pdb=" C ALA A 26 " pdb=" N TRP A 27 " ideal model delta sigma weight residual 122.12 118.41 3.71 1.06e+00 8.90e-01 1.22e+01 angle pdb=" CA ALA A 26 " pdb=" C ALA A 26 " pdb=" N TRP A 27 " ideal model delta sigma weight residual 117.30 120.98 -3.68 1.16e+00 7.43e-01 1.01e+01 angle pdb=" N VAL A 63 " pdb=" CA VAL A 63 " pdb=" C VAL A 63 " ideal model delta sigma weight residual 109.34 115.74 -6.40 2.08e+00 2.31e-01 9.47e+00 angle pdb=" O ILE A 96 " pdb=" C ILE A 96 " pdb=" N LEU A 97 " ideal model delta sigma weight residual 121.87 118.94 2.93 9.70e-01 1.06e+00 9.12e+00 angle pdb=" N GLY A 64 " pdb=" CA GLY A 64 " pdb=" C GLY A 64 " ideal model delta sigma weight residual 112.64 117.89 -5.25 1.74e+00 3.30e-01 9.10e+00 ... (remaining 5660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 2188 21.89 - 43.78: 172 43.78 - 65.67: 39 65.67 - 87.57: 10 87.57 - 109.46: 4 Dihedral angle restraints: 2413 sinusoidal: 932 harmonic: 1481 Sorted by residual: dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.25 109.46 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.85 107.47 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C6 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O4 BMA B 3 " ideal model delta sinusoidal sigma weight residual -163.34 -59.86 -103.48 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 2410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 596 0.070 - 0.140: 58 0.140 - 0.210: 4 0.210 - 0.280: 1 0.280 - 0.350: 1 Chirality restraints: 660 Sorted by residual: chirality pdb=" CAD HC6 A 603 " pdb=" CAC HC6 A 603 " pdb=" CAG HC6 A 603 " pdb=" OAE HC6 A 603 " both_signs ideal model delta sigma weight residual False 2.61 2.26 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LEU A 482 " pdb=" N LEU A 482 " pdb=" C LEU A 482 " pdb=" CB LEU A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 657 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ HC6 A 603 " -0.037 2.00e-02 2.50e+03 1.98e-02 7.83e+00 pdb=" CAM HC6 A 603 " 0.038 2.00e-02 2.50e+03 pdb=" CAN HC6 A 603 " 0.004 2.00e-02 2.50e+03 pdb=" CAO HC6 A 603 " 0.003 2.00e-02 2.50e+03 pdb=" CAP HC6 A 603 " -0.000 2.00e-02 2.50e+03 pdb=" CAQ HC6 A 603 " -0.002 2.00e-02 2.50e+03 pdb=" CAR HC6 A 603 " 0.009 2.00e-02 2.50e+03 pdb=" CAS HC6 A 603 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 457 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 458 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 452 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.027 5.00e-02 4.00e+02 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 82 2.70 - 3.25: 3911 3.25 - 3.80: 6225 3.80 - 4.35: 7865 4.35 - 4.90: 13854 Nonbonded interactions: 31937 Sorted by model distance: nonbonded pdb=" OD2 ASP A 188 " pdb="NA NA A 602 " model vdw 2.155 2.470 nonbonded pdb=" OG SER A 350 " pdb="NA NA A 602 " model vdw 2.173 2.470 nonbonded pdb=" OG SER A 346 " pdb="NA NA A 601 " model vdw 2.189 2.470 nonbonded pdb=" O VAL A 63 " pdb="NA NA A 601 " model vdw 2.232 2.470 nonbonded pdb=" OH TYR A 433 " pdb=" OD1 ASP A 512 " model vdw 2.236 3.040 ... (remaining 31932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4143 Z= 0.301 Angle : 0.758 8.976 5665 Z= 0.392 Chirality : 0.046 0.350 660 Planarity : 0.006 0.071 683 Dihedral : 17.768 109.457 1477 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.20 % Allowed : 16.39 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.39), residues: 513 helix: 1.82 (0.28), residues: 374 sheet: -3.68 (1.45), residues: 10 loop : 0.08 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.018 0.001 TYR A 175 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 1.1105 time to fit residues: 51.0208 Evaluate side-chains 36 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 373 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.096377 restraints weight = 4604.101| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.71 r_work: 0.2757 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4143 Z= 0.180 Angle : 0.582 8.038 5665 Z= 0.287 Chirality : 0.039 0.165 660 Planarity : 0.005 0.037 683 Dihedral : 11.844 74.022 657 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.41 % Allowed : 16.87 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.39), residues: 513 helix: 2.17 (0.28), residues: 365 sheet: -3.75 (1.38), residues: 10 loop : 0.23 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 27 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 395 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (ttp) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 1.0665 time to fit residues: 48.0330 Evaluate side-chains 40 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096590 restraints weight = 4599.255| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.71 r_work: 0.2746 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4143 Z= 0.180 Angle : 0.558 8.019 5665 Z= 0.277 Chirality : 0.039 0.155 660 Planarity : 0.004 0.036 683 Dihedral : 9.425 61.748 654 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.41 % Allowed : 16.87 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.39), residues: 513 helix: 2.19 (0.27), residues: 371 sheet: -3.76 (1.38), residues: 10 loop : 0.24 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 27 HIS 0.002 0.001 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7983 (t60) cc_final: 0.7355 (t-100) REVERT: A 395 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8213 (mtp) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 1.1101 time to fit residues: 51.0952 Evaluate side-chains 43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099100 restraints weight = 4606.532| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.70 r_work: 0.2798 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4143 Z= 0.155 Angle : 0.525 8.185 5665 Z= 0.261 Chirality : 0.038 0.118 660 Planarity : 0.004 0.036 683 Dihedral : 8.321 57.503 654 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.65 % Allowed : 16.63 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.39), residues: 513 helix: 2.29 (0.27), residues: 372 sheet: -3.74 (1.40), residues: 10 loop : 0.26 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.015 0.001 TYR A 67 ARG 0.001 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7980 (t60) cc_final: 0.7363 (t-100) outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 1.0157 time to fit residues: 45.7994 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100371 restraints weight = 4727.972| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.80 r_work: 0.2814 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4143 Z= 0.137 Angle : 0.497 7.993 5665 Z= 0.246 Chirality : 0.037 0.118 660 Planarity : 0.004 0.035 683 Dihedral : 7.574 56.269 654 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.17 % Allowed : 17.59 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.39), residues: 513 helix: 2.38 (0.27), residues: 373 sheet: -3.65 (1.40), residues: 10 loop : 0.36 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.015 0.001 TYR A 67 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7801 (t60) cc_final: 0.7158 (t-100) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.9956 time to fit residues: 44.9145 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.092143 restraints weight = 4471.292| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.76 r_work: 0.2772 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4143 Z= 0.179 Angle : 0.542 8.151 5665 Z= 0.272 Chirality : 0.038 0.122 660 Planarity : 0.004 0.037 683 Dihedral : 7.632 57.464 654 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.41 % Allowed : 16.63 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.39), residues: 513 helix: 2.26 (0.27), residues: 371 sheet: -3.60 (1.38), residues: 10 loop : 0.25 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.018 0.001 TYR A 67 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7962 (t60) cc_final: 0.7319 (t-100) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 1.0479 time to fit residues: 48.2106 Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.092724 restraints weight = 4522.690| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.77 r_work: 0.2790 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4143 Z= 0.167 Angle : 0.530 7.960 5665 Z= 0.265 Chirality : 0.038 0.119 660 Planarity : 0.004 0.036 683 Dihedral : 7.330 56.411 654 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.69 % Allowed : 17.59 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.39), residues: 513 helix: 2.29 (0.27), residues: 372 sheet: -3.58 (1.38), residues: 10 loop : 0.30 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7975 (t60) cc_final: 0.7329 (t-100) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 1.1244 time to fit residues: 48.1688 Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.092271 restraints weight = 4480.062| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.78 r_work: 0.2758 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4143 Z= 0.170 Angle : 0.531 8.084 5665 Z= 0.267 Chirality : 0.038 0.118 660 Planarity : 0.004 0.037 683 Dihedral : 7.157 56.389 654 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.69 % Allowed : 17.83 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.39), residues: 513 helix: 2.28 (0.27), residues: 372 sheet: -3.62 (1.38), residues: 10 loop : 0.28 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.416 Fit side-chains REVERT: A 27 TRP cc_start: 0.7965 (t60) cc_final: 0.7339 (t-100) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 1.1675 time to fit residues: 49.9384 Evaluate side-chains 39 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.434 > 50: distance: 22 - 42: 9.079 distance: 29 - 50: 10.315 distance: 33 - 56: 10.296 distance: 35 - 36: 3.927 distance: 36 - 37: 4.442 distance: 36 - 39: 3.865 distance: 37 - 38: 3.736 distance: 37 - 42: 4.936 distance: 38 - 63: 5.013 distance: 39 - 40: 4.999 distance: 39 - 41: 10.936 distance: 42 - 43: 3.321 distance: 43 - 44: 5.142 distance: 43 - 46: 3.404 distance: 44 - 45: 7.962 distance: 44 - 50: 3.602 distance: 45 - 71: 14.112 distance: 46 - 47: 7.692 distance: 46 - 48: 10.223 distance: 47 - 49: 5.347 distance: 50 - 51: 11.629 distance: 51 - 52: 4.635 distance: 51 - 54: 8.150 distance: 52 - 53: 9.231 distance: 52 - 56: 9.207 distance: 54 - 55: 20.042 distance: 56 - 57: 7.192 distance: 57 - 58: 6.478 distance: 57 - 60: 6.959 distance: 58 - 59: 8.244 distance: 58 - 63: 5.372 distance: 60 - 61: 5.474 distance: 60 - 62: 3.580 distance: 63 - 64: 3.269 distance: 64 - 65: 9.736 distance: 64 - 67: 6.344 distance: 65 - 66: 22.042 distance: 65 - 71: 12.394 distance: 67 - 68: 9.630 distance: 67 - 69: 7.054 distance: 68 - 70: 9.487 distance: 71 - 72: 9.424 distance: 72 - 73: 13.058 distance: 72 - 75: 17.267 distance: 73 - 74: 22.712 distance: 73 - 79: 19.662 distance: 75 - 76: 12.733 distance: 75 - 77: 14.018 distance: 80 - 81: 16.484 distance: 80 - 83: 18.435 distance: 81 - 82: 7.410 distance: 81 - 87: 6.283 distance: 83 - 84: 14.524 distance: 84 - 85: 17.725 distance: 84 - 86: 7.843 distance: 87 - 88: 17.644 distance: 88 - 89: 11.666 distance: 88 - 91: 29.370 distance: 89 - 90: 4.710 distance: 89 - 94: 5.025 distance: 91 - 92: 13.753 distance: 91 - 93: 7.074 distance: 94 - 95: 5.149 distance: 95 - 96: 3.574 distance: 95 - 98: 10.485 distance: 96 - 102: 5.982 distance: 97 - 127: 10.937 distance: 98 - 99: 11.842 distance: 99 - 100: 12.003 distance: 99 - 101: 11.775 distance: 102 - 103: 3.857 distance: 103 - 104: 5.491 distance: 103 - 106: 10.233 distance: 104 - 105: 4.979 distance: 104 - 110: 5.574 distance: 105 - 133: 10.095 distance: 106 - 107: 4.736 distance: 107 - 108: 11.063 distance: 108 - 109: 13.454 distance: 113 - 138: 3.283